5. Structure Manipulation Programs

This section of the manual contains a brief description of each of the TINKER structure
manipulation, geometric calculation and auxiliary programs. A detailed example showing
how to run each program is included in a later section. The programs listed below are all
part of the main, supported distribution. Additional source code for various unsupported
programs can be found in the /other directory of the TINKER distribution.

ARCHIVE

A program for concatenating TINKER cycle files into a single archive file; useful for
storing the intermediate results of minimizations, dynamics trajectories, and so on. The
archive file can be written in TINKER format, or in formats usable with MSI's InsightII
(their CAR file with .msi extension) or with XMakemol (their file format with
.xmol extension). Only active atoms are written into the InsightII and XMakemol
output files, allowing display of partial structures. The program can also extract individual
cycle files from a TINKER archive.

CORRELATE

A program to compute time correlation functions from collections of TINKER cycle files.
Its use requires a user supplied function property that computes the value of the
property for which a time correlation is desired for two input structures. A sample routine is
supplied that computes either a velocity autocorrelation function or an rms structural
superposition as a function of time. The main body of the program organizes the overall
computation in an efficient manner and outputs the final time correlation function.

CRYSTAL

A program for the interconversion of fractional and Cartesian coordinates, generation of the
unit cells from an asymmetric unit, and building a 3x3x3 crystalline block from a single unit
cell. The present version can handle about 25 of the most common space groups, others can
easily be added as needed by modification of the routine symmetry.

DIFFUSE

A program to compute the self-diffusion constant for a homogeneous liquid via the
Einstein equation. A previously saved dynamics trajectory is read in and "unfolded" to
reverse translation of molecules due to use of periodic boundary conditions. The average
motion over all molecules is then used to compute the self-diffusion constant. While the
current program assumes a homogeneous system, it should be easy to modify the code to
handle diffusion of individual molecules or other desired effects.

DISTGEOM

A program to perform distance geometry calculations using variations on the classic metric
matrix method. A user specified number of structures consistent with keyfile input distance
and dihedral restraints is generated. Bond length and angle restraints are derived from the
input structure. Trial distances between the triangle smoothed lower and upper bounds can
be chosen via any of several metrization methods, including a very effective partial random
pairwise scheme. The correct radius of gyration of the structure is automatically maintained
by choosing trial distances from Gaussian distributions of appropriate mean and width. The
initial embedded structures can be further refined against a geometric restraint-only potential
using either a sequential minimization protocol or simulated annealing.

DOCUMENT

The DOCUMENT program is provided as a minimal listing and documentation tool. It
operates on the TINKER source code, either individual files or the complete source listing
produced by the command script listing.make, to generate lists of routines,
common blocks or valid keywords. In addition, the program has the ability to output a
formatted parameter listing from the standard TINKER parameter files.

INTEDIT

A program to allow interactive inspection and alteration of the internal coordinate
definitions and values of a TINKER structure. If the structure is altered, the user has the
option to write out a new internal coordinates file upon exit.

INTXYZ

A program to convert a TINKER .int internal coordinates formatted file into a
TINKER .xyz Cartesian coordinates formatted file.

NUCLEIC

A program for automated building of nucleic acid structures. Upon interactive input of a
nucleotide sequence with optional phosphate backbone angles, the program builds internal
and Cartesian coordinates. Standard bond lengths and angles are used. Both DNA and
RNA sequences are supported as are A-, B- and Z-form structures. Double helixes of
complementary sequence can be automatically constructed via a rigid docking of individual
strands.

PDBXYZ

A program for converting a Brookhaven Protein Data Bank file (a PDB file) into a
TINKER .xyz Cartesian coordinate file. If the PDB file contains only protein/peptide
amino acid residues, then standard protein connectivity is assumed, and transferred to the
.xyz file. For non-protein portions of the PDB file, atom connectivity is determined
by the program based on interatomic distances. The program also has the ability to add or
remove hydrogen atoms from a protein as required by the force field specified during the
computation.

PROTEIN

A program for automated building of peptide and protein structures. Upon interactive input
of an amino acid sequence with optional phi/psi/omega/chi angles, D/L chirality, etc., the
program builds internal and Cartesian coordinates. Standard bond lengths and angles are
assumed for the peptide. The program will optionally convert the structure to a cyclic
peptide, or add either or both N- and C-terminal capping groups. Atom type numbers are
automatically assigned for the specified force field. The final coordinates and a sequence
file are produced as the output.

RADIAL

A program to compute the pair radial distribution function between two atom types. The
user supplies the two atom names for which the distribution function is to be computed, and
the width of the distance bins for data analysis. A previously saved dynamics trajectory is
read as input. The raw radial distribution and a spline smoothed version are then output
from zero to a distance equal to half the minimum periodic box dimension. The atom names
are matched to the atom name column of the TINKER .xyz file, independent of
atom type.

SPACEFILL

A program to compute the volume and surface areas of molecules. Using a modified
version of Connolly's original analytical description of the molecular surface, the program
determines either the van der Waals, accessible or molecular (contact/reentrant) volume and
surface area. Both surface area and volume are broken down into their geometric
components, and surface area is decomposed into the convex contribution for each
individual atom. The probe radius is input as a user option, and atomic radii can be set via
the keyword file.

SPECTRUM

A program to compute a power spectrum from velocity autocorrelation data. As input, this
program requires a velocity autocorrelation function as produced by the CORRELATE
program. This data, along with a user input time step, are Fourier transformed to generate
the spectral intensities over a wavelength range. The result is a power spectrum, and the
positions of the bands are those predicted for an infrared or Raman spectrum. However, the
data is not weighted by molecular dipole moment derivatives as would be required to
produce correct IR intensities.

SUPERPOSE

A program to superimpose two molecular structures in 3-dimensions. A variety of options
for input of the atom sets to be used during the superposition are presented interactively to
the user. The superposition can be mass-weighted if desired, and the coordinates of the
second structure superimposed on the first structure are optionally output.

SYBYLXYZ

A program for converting a TRIPOS Sybyl MOL2 file into a TINKER .xyz
Cartesian coordinate file. The current version of the program does not attempt to
convert the Sybyl atoms types into the active TINKER force field types, i.e., all
atoms types are simply set to zero.

TVIEW

This is a molecule viewing program derived from the well-know Rasmol program of Roger
Sayle. TVIEW is modified to remove most of the protein-specific options and to directly
read the TINKER .xyz file format. We hope to provide additional functionality in
future versions of TVIEW, especially the ability to animate the viewing of sequences of
coordinate snapshots from a minimization or dynamic trajectory.

XYZEDIT

A program that performs and of a variety of manipulations on an input TINKER .xyz
Cartesian coordinates formatted file. The present version of the program has the following
interactively selectable options: (1) Offset the Numbers of the Current Atoms, (2) Deletion
of Individual Specified Atoms, (3) Deletion of Specified Types of Atoms, (4) Deletion of
Atoms outside Cutoff Range, (5) Insertion of Individual Specified Atoms, (6) Replace Old
Atom Type with a New Type, (7) Assign Connectivities based on Distance, (8) Convert
Units from Bohrs to Angstroms, (9) Invert thru Origin to give Mirror Image, (10) Translate
Center of Mass to the Origin, (11) Translate a Specified Atom to the Origin, (12) Translate
and Rotate to Inertial Frame, (13) Move to Specified Rigid Body Coordinates, (14) Create
and Fill a Periodic Boundary Box, (15) Soak Current Molecule in Box of Solvent, (16)
Append another XYZ file to Current One. In most cases, multiply options can be applied
sequentially to an input file. At the end of the editing process, a new version of the original
.xyz file is written as output.

XYZINT

A program for converting a TINKER .xyz Cartesian coordinate formatted file into
a TINKER .int internal coordinates formatted file.

XYZPDB

A program for converting a TINKER .xyz Cartesian coordinate file into a
Brookhaven Protein Data Bank file (a PDB file).

XYZSYBYL

A program to convert a TINKER .xyz Cartesian coordinates file into a TRIPOS
Sybyl MOL2 file. The conversion generates only the MOLECULE, ATOM, BOND and
SUBSTRUCTURE record type in the MOL2 file. Generic Sybyl atom types are used in
most cases; while these atom types may need to be altered in some cases, Sybyl is usually
able to correctly display the resulting MOL2 file.